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Crystal structure of hen egg white lysozyme at 100 Kelvin (Duplicate)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3A8Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 295 1.2 M NaCl and 100 mM AcONa pH 4.6
Crystal Properties Matthews coefficient Solvent content 2 38.47
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.629 α = 90 b = 78.629 β = 90 c = 37.07 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS BRUKER PHOTON 100 2020-10-05 L LAUE
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER TURBO X-RAY SOURCE 1.54184
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.5 24.88 99.92 0.772 6.67 1.91 19148
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.5 24.88 0.772 6.67
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3A8Z 1.5 24.877 19148 983 99.917 0.177 0.1755 0.1841 0.2117 0.2155 11.4
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.012 0.012 -0.024
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.598 r_dihedral_angle_4_deg 16.922 r_dihedral_angle_3_deg 12.517 r_dihedral_angle_1_deg 6.718 r_lrange_it 4.043 r_lrange_other 3.954 r_scangle_it 3 r_scangle_other 2.999 r_scbond_it 2.059 r_scbond_other 2.058
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.598 r_dihedral_angle_4_deg 16.922 r_dihedral_angle_3_deg 12.517 r_dihedral_angle_1_deg 6.718 r_lrange_it 4.043 r_lrange_other 3.954 r_scangle_it 3 r_scangle_other 2.999 r_scbond_it 2.059 r_scbond_other 2.058 r_angle_refined_deg 1.795 r_angle_other_deg 1.615 r_mcangle_other 1.553 r_mcangle_it 1.551 r_mcbond_it 1.048 r_mcbond_other 0.977 r_nbd_refined 0.252 r_symmetry_nbd_other 0.198 r_symmetry_xyhbond_nbd_refined 0.18 r_nbd_other 0.177 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.084 r_symmetry_nbd_refined 0.065 r_metal_ion_refined 0.054 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1001 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SAINT data reduction